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Decoding the chromatin accessibility in Andrographis paniculata genome,a case study of genome-wide investigation of the cis-regulatory elements in medicinal plants

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Acta Pharmaceutica Sinica B 2024年第9期14卷 4179-4182页

作者： Mingkun Huang Yufang Hu Ling Zhang Hua Yang Chen Feng Chunhong Jiang Ning Xie Difa Liu Shilin Chen Jihua Wang Wei Sun Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization Lushan Botanical GardenChinese Academy of SciencesJiujiang 332900China Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine China Academy of Chinese Medical SciencesInstitute of Chinese Materia Medic1Beijing 100070China State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Institute of Chinese Materia Medic1China Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agriculture SciencesGuangzhou 510640China State Key Laboratory of Innovative Natural Medicine and TCM Injections Jiangxi Qingfeng Pharmaceutical Co.Ltd.Ganzhou 341008China

To the Editor:Medicinal plants have the ability to synthesize a large number of pharmaceutical metabolites,the production and regulation of which are influenced by both intrinsic signals(e.g.,the spatial and temporal stage)and extrinsic environmental conditions(e.g.,temperature,light availability,and water availability)^(1).According to the Encyclopedia of DNA elements(ENCODE)project^(2),accessible chromatin regions(ACRs)served essential roles in maintaining the genome architecture and gene regulation in both mammals and ***,identifying ACRs within medicinal plant genomes remains a challenge,as genomic sequences have been determined for numerous species yet the characterization of such functional elements *** this study,we selected Andrographis paniculata(APA)^(3) as a model system to map ACRs genome-wide by the assay for transposase-accessible chromatin with sequencing(ATAC-seq)*** aimed to uncover the genomic features of ACRs as well as their association with the expression of genes involved in secondary metabolite biosynthesis(e.g.,andrographolide)within medicinal plants(Supporting Information Fig.S1).

关键词： Andrographis paniculata Chromatin accessibility Medicinal plant Epigenetics ENCODE cis-regulatory elements

Global identification of gene networks and cis-regulatory elements for cold responses in zebrafish

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Global identification of gene networks and cis-regulatory el...

Inducible CRISPRa screen identifies putative enhancers

2014年中国水产学会学术年会

作者： Peng Hu Mingli Liu Shanghai Ocean University

Here we profiled transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures, from normal 28℃ to mild（18°C） and server cold（9°C） by RNA-seq. Tissues vary in the number of cold responsive genes in which kidney appeared mostly sensitive while brain the least. Fuzzy k-means clustering revealed 34 gene clusters of distinct expression patterns, demonstrated diverse tissue-specific responses in conjunction with multiple aspects of ubiquitous cross-tissue responses to cold. 31 GO terms are over-represented upon cold treatment, involving in basic cellular processes such as RNA splicing and proton transport as well tissue-specific processes such as ‘negative regulation of endopeptidase’ in kidney. To elucidate the cis-regulatory elements governing the concerted cold responses, promoters of genes that demonstrated strong co-regulation are analyzed by an enriched motif discovery program DREME. 11 motifs, 6 known and 5 novel, are identified which are born to genes involving in 16 GO terms identified above. Some known motifs, such as the AP-1 and STAT1 binding sites have known to be stress responsive. A novel motif, AGMAACCA, is experimentally verified to be the binding site of transcription regulator BCL6, responding to cold challenges through a de-depression mechanism.

关键词： Transcriptional Cold Temperatures RNA-seq Distinct Expression cis-regulatory elements Motifs

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Journal of Genetics and Genomics 2021年第10期48卷 917-927页

作者： Zhongye Dai Rui Li Yuying Hou Qian Li Ke Zhao Ting Li Mulin Jun Li Xudong Wu State Key Laboratory of Experimental Hematology The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical EpigeneticsTianjin Key Laboratory of Cellular Homeostasis and Human DiseasesDepartment of Cell BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjin 300070China Department of Pharmacology Tianjin Key Laboratory of Medical EpigeneticsTianjin Medical UniversityTianjin 300070China Department of Neurosurgery Tianjin Medical University General HospitalTianjin 300052China Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants Tianjin 300450China

Enhancers are critical cis-regulatory elements that regulate spatiotemporal gene expression and control cell ***,the identification of enhancers in native cellular contexts still remains a ***,we develop an inducible CRISPR activation(CRISPRa)system by transgenic expression of doxycycline(Dox)-inducible dCas9-VPR in mouse embryonic stem cells(iVPR ESC).With this line,a simple introduction of specific guide RNAs targeting promoters or enhancers allows us to realize the effect of CRISPRa in an inducible,reversible,and Dox concentration-dependent *** advantage of this system,we induce tiled CRISPRa across genomic regions(105 kilobases)surrounding T(Brachyury),one of the key mesodermal development regulator ***,we identify several CRISPRa-responsive elements with chromatin features of putative enhancers,including a region the homologous sequence in which humans harbors a body height risk *** deletion of this region in ESC does affect subsequent T gene activation and osteogenic ***,our inducible CRISPRa ESC line provides a convenient platform for high-throughput screens of putative enhancers.

关键词： CRISPR activationl cis-regulatory elements Enhancerl Screen

Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates

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Science China(Life Sciences) 2023年第10期66卷 2399-2414页

作者： Zeng Wang Changjun Peng Wei Wu Chaochao Yan Yunyun Lv Jia-Tang Li CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengdu 610041China University of Chinese Academy of Sciences Beijing 100049China College of Life Science Neijiang Normal UniversityNeijiang 641100China Southeast Asia Biodiversity Research Institute Chinese Academy of SciencesYezin Nay Pyi Taw 05282Myanmar

Limb loss shows recurrent phenotypic evolution across squamate ***,based on three de novo-assembled genomes of limbless lizards from different lineages,we showed that divergence of conserved non-coding elements(CNEs)played an important role in limb *** CNEs were associated with genes required for limb initiation and outgrowth,and with regulatory signals in the early stage of limb ***,we identified the extensive existence of insertions and deletions(In Dels)in the CNEs,with the numbers ranging from 111 to *** of these CNEs with In Dels were lineagespecific in the limbless *** genes of these In Del CNEs were important to early limb formation,such as Tbx4,Fgf10,and *** on functional experiments,we found that nucleotide mutations and In Dels both affected the regulatory function of the *** study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element In Dels in phenotypic evolution.

关键词： squamates limb loss cis-regulatory elements early limb development

Distinct Role of Core Promoter Architecture in Regulation of Light-Mediated Responses in Plant Genes

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Molecular Plant 2014年第4期7卷 626-641页

作者： Rakesh Srivastava Krishan Mohan Rai Meenal Srivastava Verandra Kumar Bindu Pandey Sudhir P. Singh Sumit K. Bag Brahma Deo Singh Rakesh Tuli Samir V. Sawant Plant Molecular Biology and Genetic Engineering Division CSIR-National Botanical Research Institute Rana Pratap Marg Lucknow-226001 (U.R) India School of Biotechnology Faculty of Science Banaras Hindu University Varanasi India National Agri-Food Biotechnology Institute (DBT) C-127 Industrial Area Phase VIII Mohali India Academy of Scientific & Innovative Research New Delhi India

In the present study, we selected four distinct classes of light-regulated promoters. The light-regulated promoters can be distinctly grouped into either TATA-box-containing or TATA-less （initiator-containing） promoters. Further, using either native promoters or their swapped versions of core promoter elements, we established that TATA-box and Inr （Initiator） elements have distinct mechanisms which are involved in light-mediated regulation, and these elements are not swappable. We identified that mutations in either functional TATA-box or Inr elements lead to the formation of nucleosomal structure. The nucleotide diversity in either the TATA-box or Inr element in Arabidopsis ecotypes proposes that the nucleotide variation in core promoters can alter the gene expression. We show that motif overrepresentation in light-activated promoters encompasses different specific regulatory motifs present downstream of TSS （transcription start site）, and this might serve as a key factor in regulating light promoters which are parallel with these elements. Finally, we conclude that the TATA-box or Inr element does not act in isolation, but our results clearly suggests the probable involvement of other distinct core promoter elements in concurrence with the TATA-box or Inr element to impart selectivity to light-mediated transcription.

关键词： TATA-box initiator element nucleosome cis-regulatory elements nucleotide polymorphism light transcription.

Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis

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Journal of Animal Science and Biotechnology 2023年第4期14卷 1344-1362页

作者： Jie Cheng Xiukai Cao Xiaogang Wang Jian Wang Binglin Yue Wei Sun Yongzhen Huang Xianyong Lan Gang Ren Chuzhao Lei Hong Chen College of Animal Science and Technology Northwest A&F UniversityNo.22 Xinong RoadYangling districtYanglingShaanxi province 712100China Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China Yangzhou UniversityYangzhou 225009China Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Southwest Minzu UniversityChengdu 610225China College of Animal Science and Technology Yangzhou UniversityYangzhou 225009China College of Animal Science Xinjiang Agricultural UniversityUrumqi 830052China

Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in ***-dimensional genome structure is confirmed to be an important layer of transcription *** genome-wide interaction data of several livestock species have already been produced,the genome structure states and its regulatory rules in cattle muscle are still *** Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle(Bos taurus).We showed that compartments,topologically associating domains(TADs),and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle ***,we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection *** further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast *** Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology,which will benefit the progress of genetic improvement of beef cattle.

关键词： Cattle cis-regulatory elements Muscle Selection sweep 3D genome

A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana

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Journal of Integrative Plant Biology 2014年第6期56卷 527-538页

作者： Mohammad Amin Omidbakhshfard Flavia Vischi Winck Samuel Arvidsson Diego M.Ria?o-Pachón Bernd Mueller-Roeber University of Potsdam Institute of Biochemistry and Biology Potsdam-Golm 14476 Germany Max-Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476 Germany Brazilian Bioethanol Science and Technology Laboratory (CTBE) Brazilian Center of Research in Energy and Materials (CNPEM) Campinas Brazil

The control of gene expression by transcriptional regulators and other types of functional y relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in al organisms. DNA transactions require the control ed interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions （NDRs） of the chromatin. Formaldehyde-assisted isolation of regulatory elements （FAIRE） has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successful y employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol wil be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.

关键词： Arabidopsis thaliana chromatin cis-regulatory elements epigenomics FAIRE-qPCR FAIRE-seq gene expression gene regulatory network transcription factor

Profiling Chromatin Accessibility at Single-cell Resolution

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Genomics, Proteomics & Bioinformatics 2021年第2期19卷 172-190页

作者： Sarthak Sinha Ansuman T.Satpathy Weiqiang Zhou Hongkai Ji Jo A.Stratton Arzina Jaffer Nizar Bahlis Sorana Morrissy Jeff A.Biernaskie Department of Comparative Biology&Experimental Medicine Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAB T2N 4N1Canada Department of Pathology Stanford University School of MedicineStanfordCA 94305USA Department of Biostatistics Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMD 21205USA Alberta Children’s Hospital Research Institute University of CalgaryCalgaryAB T2N 4N1Canada Hotchkiss Brain Institute University of CalgaryCalgaryAB T2N 4N1Canada Arnie Charbonneau Cancer Institute University of CalgaryCalgaryAB T2N 4Z6Canada Department of Biochemistry and Molecular Biology Cumming School of MedicineUniversity of CalgaryCalgaryAB T2N 4N1Canada

How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity,and enable complex fate decisions are important open *** key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin ***-wide chromatin accessibility measurements can impart insights into regulatory sequences(in)accessible to DNA-binding proteins at a single-cell *** review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing(scATAC-seq)in a scalable *** also covers joint profiling of chromatin with transcriptome/proteome measurements,computational strategies to integrate multi-omic measurements,and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic *** refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.

关键词： Single-cell ATAC-seq Gene regulation Epigenetics Single-cell multi-omics cis-regulatory elements

Characterization of the Tomato Prosystemin Promoter:Organ-specific Expression,Hormone Specificity and Methyl Jasmonate Responsiveness by Deletion Analysis in Transgenic Tobacco Plants

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Journal of Integrative Plant Biology 2012年第1期54卷 15-32页

作者： Hamlet Avilés-Arnaut John Paul Délano-Frier Center of Research and Advanced Studies (Cinvestav) at Irapuato:Unit for Plant Biotechnology and Genetic Engineering

Tomato systemin is a bioactive peptide that regulates the systemic activation of wound-responsive genes. It is released from its 200 amino acid precursor called prosystemin. Initial tissue-localization and hormone-induced expression assays indicated that the tomato prosystemin gene （SIPS） accumulates mainly in floral tissues and in response to exogenous abscisic acid and methyl jasmonate （MeJA） treatments, respectively. Later, the promoter regions of the PS gene in tomato （Solanum lycopersicum L. cv. Castlemart）, pepper （Capsicum annuum） and potato （Solanum tuberosum） were isolated and an in silico analysis of the SIPS promoter revealed an over-representation of stress- and MeJA-responsive motifs. A subsequent 5＇ deletion analysis of the SIPS promoter fused to the/^-glucuronidase reporter （GUS） gene showed that the -221 to ＋40 bp proximal SIPS promoter region was sufficient to direct the stigma, vascular bundle-specific and MeJA-responsive expression of GUS in transgenic tobacco plants. Important ***-specific, light- and MeJA-responsive cis-elements were also present in this region. These findings provide relevant information regarding the transcriptional regulation mechanisms of the SIPS promoter operating in transgenic tobacco plants. They also suggest that its Ussue-specificity and inducible nature could have wide applicability in plant biotechnology.

关键词： cis-regulatory elements flower specific jasmonic acid methyl jasmonate promoter analysis prosystemin wound-responsive genes.